[English] 日本語
Yorodumi
- PDB-7tuo: Crystal structure analysis of human USP28 complex with a compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tuo
TitleCrystal structure analysis of human USP28 complex with a compound
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE/HYDROLASE INHIBITOR / deubiquitinase / inhibitor / protein-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cell population proliferation / nuclear body / Ub-specific processing proteases / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase ...: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / UBA-like superfamily / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-KL9 / Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of human USP28 complex with a compound
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8514
Polymers44,9721
Non-polymers8793
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.640, 114.640, 114.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1081-

HOH

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28


Mass: 44972.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-KL9 / 7-amino-N-(2-{4-[(1R,3s,5S)-8-azabicyclo[3.2.1]octan-3-yl]phenyl}ethyl)-3-methylthieno[2,3-b]pyrazine-6-carboxamide


Mass: 421.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4M Sodium maleic acid, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.96→81.06 Å / Num. obs: 36300 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 36.62 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.112 / Net I/σ(I): 17.3 / Num. measured all: 496809
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.96-1.99141.42500517920.5942.22499.9
5.32-81.1312.555.52419719420.010.035100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HEH

6heh


Resolution: 1.96→81.06 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1824 5.03 %
Rwork0.1777 34445 -
obs0.1791 36269 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.13 Å2 / Biso mean: 47.6014 Å2 / Biso min: 19.6 Å2
Refinement stepCycle: final / Resolution: 1.96→81.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 115 205 2950
Biso mean--61.38 48.25 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.96-2.010.34631410.309226222763
2.01-2.070.27811330.247926262759
2.07-2.140.24731330.224326242757
2.14-2.220.27351520.199426032755
2.22-2.30.20991120.207926462758
2.3-2.410.25971380.207626332771
2.41-2.540.23341250.222126572782
2.54-2.690.25631220.198126552777
2.7-2.90.23031390.18426472786
2.9-3.190.23191780.188726142792
3.2-3.650.19611290.147426762805
3.66-4.610.15811700.142726682838
4.61-81.060.16921520.168627742926
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.05891.0571-0.27032.31870.02661.1883-0.00980.13140.3267-0.1960.04020.2159-0.2206-0.1025-0.00010.29980.05860.01240.34050.06550.37488.540729.6779-15.6589
20.3877-0.0466-0.42670.2363-0.08770.5524-0.07530.2608-0.09840.08030.05830.2910.2451-0.50320.00020.3647-0.065-0.00160.45760.01960.3448-1.02369.2733-17.752
31.0410.7802-0.5322.1248-0.73051.95880.02230.2476-0.0545-0.02560.04550.56360.0424-0.57480.00760.31480.0173-0.03140.41510.0280.3491-3.18559.6094-10.1027
41.6391.69150.66412.1844-0.08242.24070.0922-0.20370.33190.2147-0.03480.053-0.23380.07160.00110.28010.00330.02370.30150.01880.293310.452821.6193-3.2172
50.60990.509-0.14270.77-0.46930.40350.0226-0.10660.09150.0852-0.0285-0.0723-0.15820.17670.0010.32670.01060.01230.35070.02230.364512.468118.1124-8.9695
61.2403-0.2106-0.14821.0437-0.59460.88860.3664-0.45890.69780.23250.09590.1153-0.9787-0.2670.00110.4924-0.04730.08530.513-0.07610.620625.373845.5454-4.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 325 )A149 - 325
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 368 )A326 - 368
3X-RAY DIFFRACTION3chain 'A' and (resid 369 through 582 )A369 - 582
4X-RAY DIFFRACTION4chain 'A' and (resid 583 through 625 )A583 - 625
5X-RAY DIFFRACTION5chain 'A' and (resid 626 through 674 )A626 - 674
6X-RAY DIFFRACTION6chain 'A' and (resid 675 through 699 )A675 - 699

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more